Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches
High-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2014-01-01
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| Series: | Pathogens |
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| Online Access: | http://www.mdpi.com/2076-0817/3/1/36 |
| _version_ | 1811302473524051968 |
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| author | Dongsheng Che Mohammad Shabbir Hasan Bernard Chen |
| author_facet | Dongsheng Che Mohammad Shabbir Hasan Bernard Chen |
| author_sort | Dongsheng Che |
| collection | DOAJ |
| description | High-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes, we can discover that pathogenic genomic regions in many pathogenic bacteria are horizontally transferred from other bacteria, and these regions are also known as pathogenicity islands (PAIs). PAIs have some detectable properties, such as having different genomic signatures than the rest of the host genomes, and containing mobility genes so that they can be integrated into the host genome. In this review, we will discuss various pathogenicity island-associated features and current computational approaches for the identification of PAIs. Existing pathogenicity island databases and related computational resources will also be discussed, so that researchers may find it to be useful for the studies of bacterial evolution and pathogenicity mechanisms. |
| first_indexed | 2024-04-13T07:28:40Z |
| format | Article |
| id | doaj.art-01aa5cfb22284aef95def81f4d101769 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-04-13T07:28:40Z |
| publishDate | 2014-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-01aa5cfb22284aef95def81f4d1017692022-12-22T02:56:24ZengMDPI AGPathogens2076-08172014-01-0131365610.3390/pathogens3010036pathogens3010036Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational ApproachesDongsheng Che0Mohammad Shabbir Hasan1Bernard Chen2Department of Computer Science, East Stroudsburg University of Pennsylvania, East Stroudsburg, PA 18301, USADepartment of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USADepartment of Computer Science, University of Central Arkansas, Conway, AR 72035, USAHigh-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes, we can discover that pathogenic genomic regions in many pathogenic bacteria are horizontally transferred from other bacteria, and these regions are also known as pathogenicity islands (PAIs). PAIs have some detectable properties, such as having different genomic signatures than the rest of the host genomes, and containing mobility genes so that they can be integrated into the host genome. In this review, we will discuss various pathogenicity island-associated features and current computational approaches for the identification of PAIs. Existing pathogenicity island databases and related computational resources will also be discussed, so that researchers may find it to be useful for the studies of bacterial evolution and pathogenicity mechanisms.http://www.mdpi.com/2076-0817/3/1/36genomic islandspathogenicity islandscomputational methodsgenomic signaturemobility genevirulence factorspathogenicity island database |
| spellingShingle | Dongsheng Che Mohammad Shabbir Hasan Bernard Chen Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches Pathogens genomic islands pathogenicity islands computational methods genomic signature mobility gene virulence factors pathogenicity island database |
| title | Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches |
| title_full | Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches |
| title_fullStr | Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches |
| title_full_unstemmed | Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches |
| title_short | Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches |
| title_sort | identifying pathogenicity islands in bacterial pathogenomics using computational approaches |
| topic | genomic islands pathogenicity islands computational methods genomic signature mobility gene virulence factors pathogenicity island database |
| url | http://www.mdpi.com/2076-0817/3/1/36 |
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